GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Pseudomonas fluorescens FW300-N2C3

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate AO356_05335 AO356_05335 ABC transporter ATP-binding protein

Query= uniprot:D8J1T6
         (255 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_05335
          Length = 255

 Score =  246 bits (627), Expect = 4e-70
 Identities = 122/253 (48%), Positives = 171/253 (67%), Gaps = 1/253 (0%)

Query: 1   MSQTLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTG 60
           MS+ +LK+ ++S RFGGL A+NGV +T++  Q+  LIGPNGAGKTT FN +TG YQP  G
Sbjct: 1   MSREILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGG 60

Query: 61  TFELDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRH 120
           T  LDG+P      H +A+ G+ RTFQN+RLF +MT +EN+++  H     N F  +F+ 
Sbjct: 61  TILLDGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKT 120

Query: 121 KAAREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEP 180
            A R+ E    E ++  LD V + +FA RTA  L+YG QRRLEIAR + T P++L LDEP
Sbjct: 121 PAFRKSEREAMEYAEYWLDKVNLTEFANRTAGTLAYGQQRRLEIARCMMTRPRILMLDEP 180

Query: 181 AAGMNATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPAD 239
           AAG+N  E   L+ L+  ++ E   T+LLIEHD+KL+M + + I V++ G P+A+G P  
Sbjct: 181 AAGLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQ 240

Query: 240 VQKNPAVIEAYLG 252
           ++ NP VI+AYLG
Sbjct: 241 IRDNPEVIKAYLG 253


Lambda     K      H
   0.320    0.138    0.394 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 198
Number of extensions: 9
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 255
Length of database: 255
Length adjustment: 24
Effective length of query: 231
Effective length of database: 231
Effective search space:    53361
Effective search space used:    53361
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory